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- PDB-6r4c: Aurora-A in complex with shape-diverse fragment 57 -

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Basic information

Entry
Database: PDB / ID: 6r4c
TitleAurora-A in complex with shape-diverse fragment 57
ComponentsAurora kinase A
KeywordsTRANSFERASE / Ser/Thr protein kinase Allosteric site
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / positive regulation of mitotic nuclear division / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein stability / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / kinetochore / spindle / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-JRQ / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBayliss, R. / McIntyre, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K016903 United Kingdom
CitationJournal: Chemistry / Year: 2019
Title: Construction of a Shape-Diverse Fragment Set: Design, Synthesis and Screen against Aurora-A Kinase.
Authors: Zhang, R. / McIntyre, P.J. / Collins, P.M. / Foley, D.J. / Arter, C. / von Delft, F. / Bayliss, R. / Warriner, S. / Nelson, A.
History
DepositionMar 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8378
Polymers32,9651
Non-polymers8737
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-54 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.586, 81.586, 175.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-504-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aurora kinase A / / Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase aurora-A


Mass: 32964.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 91 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-JRQ / ethyl 2-[(2~{R})-1-[(4-methylphenyl)methyl]-3-oxidanylidene-piperazin-2-yl]ethanoate


Mass: 290.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.04→29.89 Å / Num. obs: 22811 / % possible obs: 99.8 % / Redundancy: 18.9 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Net I/σ(I): 32.5
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1593 / CC1/2: 0.935 / Rpim(I) all: 0.24 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→29.885 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.42
RfactorNum. reflection% reflection
Rfree0.2257 1152 5.07 %
Rwork0.1856 --
obs0.1877 22743 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→29.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 53 84 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092253
X-RAY DIFFRACTIONf_angle_d1.1033061
X-RAY DIFFRACTIONf_dihedral_angle_d16.481836
X-RAY DIFFRACTIONf_chiral_restr0.052329
X-RAY DIFFRACTIONf_plane_restr0.005387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0403-2.13320.26581180.21872601X-RAY DIFFRACTION99
2.1332-2.24560.24191320.20782642X-RAY DIFFRACTION100
2.2456-2.38620.25441360.20032658X-RAY DIFFRACTION100
2.3862-2.57040.25171450.21072653X-RAY DIFFRACTION100
2.5704-2.82890.27191460.21462686X-RAY DIFFRACTION100
2.8289-3.23780.25921600.21612682X-RAY DIFFRACTION100
3.2378-4.07770.23841510.1822753X-RAY DIFFRACTION100
4.0777-29.88830.18141640.15662916X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.85410.4137-0.22471.8719-0.39490.962-0.02730.0526-0.3886-0.2370.0501-0.22130.29320.2022-0.02670.3316-0.0139-0.01230.3523-0.11830.3651-0.158121.749-11.8018
24.67831.2993-1.20976.4964-2.79925.5019-0.43080.7928-1.1732-0.95180.12430.07340.0136-1.01010.13310.5161-0.0082-0.03960.5883-0.33370.6469-16.04119.9972-16.9219
32.7259-1.0503-0.72.09690.09770.55790.04330.2476-0.0527-0.12980.0459-0.00020.0528-0.0741-0.06850.2904-0.0026-0.00540.3932-0.03970.2605-14.299132.6634-10.9819
41.86590.30171.02941.94750.47122.73040.16840.0786-0.28290.0499-0.09530.08610.3452-0.438-0.06450.2633-0.0413-0.01230.3378-0.03970.3357-27.577531.9252-3.753
53.39-1.02751.16881.9137-1.92543.2324-0.3227-0.5437-0.08350.33410.18450.12320.0344-0.56480.20590.36170.00050.11250.3929-0.08160.381-28.750230.40057.765
62.35960.2960.06083.43670.47652.60590.08320.21870.4546-0.2792-0.1270.4388-0.2533-0.36780.08650.26120.0548-0.01760.3325-0.00640.3513-29.365345.4302-4.9669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 172 )
2X-RAY DIFFRACTION2chain 'A' and (resid 173 through 187 )
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 287 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 324 )
5X-RAY DIFFRACTION5chain 'A' and (resid 325 through 343 )
6X-RAY DIFFRACTION6chain 'A' and (resid 344 through 391 )

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